


Secrets Of Hydra

by GayRainbowBridge



Series: Stony Stories/Oneshots [2]
Category: Marvel Cinematic Universe
Genre: Alpha Steve Rogers, Alpha/Beta/Omega Dynamics, Angst and Hurt/Comfort, Emotional Hurt/Comfort, Hydra (Marvel), Implied/Referenced Torture, M/M, Oblivious Tony Stark, Protective Steve Rogers, Rape/Non-con Elements, Secrets, Suspicions, Tattoos, Tony Stark Needs a Hug, Violence
Language: English
Status: In-Progress
Published: 2021-02-01
Updated: 2021-02-01
Packaged: 2021-03-12 06:08:01
Rating: Mature
Warnings: Rape/Non-Con
Chapters: 5
Words: 4,227
Publisher: archiveofourown.org
Story URL: https://archiveofourown.org/works/29130795
Author URL: https://archiveofourown.org/users/GayRainbowBridge/pseuds/GayRainbowBridge
Summary: Tony has a secret. A secret that he will never tell the other Avengers, especially not Steve. He will take the secret to the grave, even if it means he's completely alone for the rest of his life.But what happens when one day Bruce, a beta of the pack, sees something that makes him fear his best friend.What happens when Bruce tells the others what he saw? What happens when the truth finally comes out?
Relationships: Steve Rogers/Tony Stark
Series: Stony Stories/Oneshots [2]
Series URL: https://archiveofourown.org/series/2099157
Comments: 4
Kudos: 38





	1. Chapter 1

Bruce went downstairs to Tony's lab which the man had been in for almost three days straight. The other team mates were worried about the alpha and it wasn't healthy for the man to be down in his lab for such long periods of time.

So the team elected Bruce to go down to the lab and check on him to make sure he wasn't dead.

Cause that's what friends are for, right?

He went into the lab to find Tony bent over his work table working on another design to improve Clint's arrow accuracy.

Tony looked up when the door opened, bags under his eyes from lack of sleep and his hands dirty and grimy from working in the lab for so long without a shower. His clothes were worn and dirty with grease and his pants were torn in some places. He obviously hadn't eaten in a while but that did nothing to the grin that Tony sent his way.

"Hey, Bruce! I was wondering when you'd visit me? It's kinda lonesome down here," Tony said in greeting.

Bruce gave a wry smile at his best friend. "Hi, Tony. I just came down to check if you were still alive. Haven't seen you in a while. How are you?"

Tony grinned a little manically. "Yeah, great! I've almost finished Clint's new arrow design. Just need to find the right arrow head. Also, could you get me some coffee? I ran out and I really need some more so I can finish-"

"Tony," Bruce cut off Tony's rambling with a sigh. "You've been down here for days! Take a break and have something to eat. You're getting skinny. And you need a shower because, no offense, but you stink. Then go to sleep already! I know for a fact that you haven't slept in at least three days!"

"How so?" Tony said with a challenge in his tone.

Bruce raised an eyebrow. "Jarvis?"

"Mr Stark has been awake for the last seventy six hours, fourteen minutes and thirty two seconds," Jarvis supplied instantly before Tony could stop him.

"Jarvis!" Tony shouted at the IA.

"Terribly sorry, Sir. But I do agree with Dr Banner. You are lacking in both sleep and substance. A break would do you some good."

"I'm fine, okay? Just give me a coffee and a sandwich and I'll be as right as rain!" Tony stated, making Bruce sigh once again.

"Please, Tony. Just take a break? Have a bite, take a shower, go to sleep and then you can go back to hiding in your lab and avoiding everyone," Bruce tried to convince the stubborn Alpha.

Tony was shaking his head before Bruce had even finished talking. "Nope. Sorry Brucey Bio. No can do. I'm on a tight schedule as it is and I just got tons of work just piling up so-" Tony turned his back on Bruce, still rambling as he walked over to one of the shelves across the room.

Bruce uttered a soft sigh watching as his friends got to the shelves, hearing a low curse when the genius reached up for a box on the top shelf. Bruce probably would have teased Tony for his height if it wasn't such a sore subject for Tony.

As Tony stretched up, his shirt riding up on him showing his lower back as he reached for the box and Bruce's blood turned to ice.

On Tony's lower back was a symbol that seemed to be branded on the geniuses back. But it wasn't the fact that it seemed to have been burnt into Tony's skin that worried Bruce. It was the fact that the symbol burnt into Tony's skin was...

...a Hydra symbol.

Bruce stared at the mark in shock, not comprehending what he was seeing. It couldn't be a Hydra symbol! That was only branded on people when they were followers of Hydra. And Tony wasn't a follower to Hydra! He couldn't be! He was part of the Avengers! He would never betray them for Hydra! He could never be part of Hydra!

...couldn't he?

Bruce didn't react quick enough as Tony managed to grab the box bringing it down from the shelve making his shirt fall, hiding the brand from view as he turned to find Bruce looking at him in horror.

"What's wrong? Do I really smell that bad?" He laughed at his own joke but Bruce didn't answer. Tony frowned, placing the box gently on the bench. "Hey? You alright?" He asked, seeming to be getting worried now.

Bruce tried to appear normal, making his expression smooth over though he doubted he managed to do anything but make his face twitch weirdly.

"I-I'm fine. Um, just ah, think about what I said. I gotta go do help Natasha with something," Bruce managed to get out before hurrying from the room quickly.

Tony watched his friend go, confusion written all over his face, before shrugging, brushing it off as he went back to his project.

As soon as he was sure he was out of Tony's earshot he spoke aloud. "Jarvis, get the other Avengers to meet me in the main room please. Except Tony," Bruce called to the AI, sure the machine wouldn't alert his creator. It was only meant to if Tony's life was in danger.

"Of course, Dr Banner," Jarvis replied curtly.


	2. Chapter 2

In no less than five minutes the rest of the Avengers, minus Tony, were sitting in the main room, watching Bruce pace up and down in agitation.

"Bruce, just calm down and tell us what happened," Natasha said soothingly to the scientist.

Bruce sighed, trusting his fingers together with nerves and fear. "I'm sorry, I just ... I cant believe Tony would do this!"

Steve frowned at him. "Do what? What are you talking about?"

"I-" Bruce choked, shaking his head.

"Bruce, what did Tony do?" Natasha asked slowly.

"I-Im not sure," Bruce admitted, chewing his lip.

"Just tell us what happened?" Natasha told him gently. The scientist took a few deep breaths, calming down slightly.

"I-I went down to check on him, you know cause he hasn't been taking care of himself. So I tried convincing him to take a break but he wouldn't," Bruce swallowed. He-he went to grab something from a shelf and his shirt went up his back and-"

He stopped feeling slightly sick.

Natasha seemed to notice. "Deep breathes, Bruce. It's okay."

Bruce nodded, taking slow steady breathes once again before he continued, pushing through it determinedly. "He has a brand on his back. It's burnt into his skin. It-" he closed his eyes not wanting to see the others' reactions to the news. "It was the Hydra symbol."

Dead silence. That's all he heard.

He opened his eyes and looked at them all. They either had looks of utter shock or disgust.

"That's not possible," Steve breathed, shaking his head. "There's no way."

"Why not?" Clint asked, looking at Steve. "For all we know he could be!"

"Wait, I do not understand," Thor said with a frown. "What would a branded Hydra symbol mean?"

Bruce rubbed his eyes tiredly. "It means that you're a follower of Hydra. That you work for them. I think that-that Tony might be working undercover for them."

"But he can't be!" Steve protested again.

"Why not? Why are you so damn sure that he's not a part of Hydra?" Clint demanded of the super soldier.

"I-I just know, okay?" Steve said not meeting any of the eyes watching him curiously.

Natasha frowned at him knowing that something was off. "Steve. What aren't you telling us?"

Steve bit his lip before sighing, defeated. They would only pry him for information. "Hydra killed Tony's parents."

The other Avengers stared at him.

"How-how do you even know that?" Bruce asked a little shakily.

"I-I saw it in a document. Fury gave it to me by accident when he was trying to talk me into the Avengers and explain who you guys were and such," Steve explained with reluctance.

"Does Tony know this?" Bruce asked, heart clenching for his friend...or who he thought was a friend.

"I-I don't know. I don't think so," Steve said, a little unsure.

"If he doesn't know then he would have no reason to _not_ join Hydra," Clint countered.

"He's not Hydra!" Steve said angrily. He couldn't believe that Tony could work for Hydra. The very thought of it was insane! How could they possibly believe this?

"Are you sure it wasn't something else, Bruce?" Natasha asked, obviously sensing Steve getting frustrated. A worked up super soldier was not what they needed right now. "Perhaps a tattoo that simply looked like a Hydra symbol? Are you completely sure it was what you think it is?"

Bruce shook his head sadly. "I-I wish I could tell you different but I'm a hundred percent sure it was the Hydra symbol."

He gave Steve an apologetic look but Steve wouldn't meet his eyes. He didn't want to believe this is true.

"Okay, look. Let's not jump to conclusions-"

"Too late," Clint interrupted Natasha.

She glared at him before continuing. "We don't know a hundred percent that he's part of Hydra. I'm sure there's a reason for this. We just need to stay calm about it. Confronting Tony will only make things worse."

"What about Fury? He'll want to hear about this," Bruce pointed out.

"Well keep it just between us for the now," she said looking at each of the others making sure they nodded in agreement.

"But, how do we find out that he's Hydra-?"

"He's _not_ Hydra!" Steve said again, over Clint.

"Fine! How do we find out if he is or _isn't_ Hydra? Happy?" He asked, glaring at Steve.

"Stop it you two,"Natasha said sternly and the pair looked away from each other. "Fighting will get us nowhere, okay? We just have to be careful and keep an eye on him, understand?"

The others nodded before their understanding freezing as a voice spoke from the doorway.

"Keep an eye on who?"

**Notes for the Chapter:**

> ✒Oop...caught out✒


	3. Chapter 3

All the Avengers turned as one to look over at the doorway. Their eyes widened in shock and some, in fear.

Tony stood looking at them all, curiosity in his brown eyes. Steve couldn't help but feel guilty as he stared at his friend. Someone who might not even be his friend. Someone he might not know at all.

Steve swallowed hard, glancing at the others for help.

Natasha spoke into the awkward silence. "On Clint. He's been feeling under the weather. We need to keep an eye on him to make sure he doesn't get any more sick because I need him for a mission next week," she lied easily, her face portraying no other emotion besides concern.

Clint nodded quickly. "Yeah, that's right." He faked a cough.

"Um...okay?" Tony gave an unsure sort of smile.

Steve and Bruce glanced at each other. How much had Tony heard? Was he faking being oblivious?

"Anyway, I uh, thought about what you said, Bruce," Tony continued after a slight pause, "and you're right. I should get out of the lab for a bit. I even thought maybe, I could go out for a while? Like, there's a new coffee shop down the road from here. I could go there, stretch my legs."

Bruce looked surprised. "Really?"

"I mean, yeah," Tony shifted uncomfortably. "Did you maybe...wanna come with?"

The others looked shocked at the question. It was one thing for Tony to be willing to go outside for a while. It was something completely else for Tony to want company and be social.

Bruce looked almost as uncomfortable as Tony. Bruce was obviously still thinking about the Hydra mark and didn't want to go anywhere with Tony. But he couldn't say that.

Steve jumped in. "Bruce has to do work for Shield. But maybe if you want I can go with you?"

Tony looked surprised but then gave a slight smile. "Alright, cool. I'll uh, get my coat and we'll go?"

Steve nodded mutely and Tony turned and left. As soon as his footsteps receded, Steve turned to the others who were looking at him in shock.

"Why did you ask to go?" Clint said before anyone could say a word.

"Because Bruce was uncomfortable. He didn't want to go with Tony," Steve said.

Bruce looked down. "I just don't know what to think. I thought I knew Tony. Now I don't know what to think."

Steve looked at him with concern. "I understand, Bruce. It's not your fault. We'll find out the truth."

"Do you think he heard us talking about him before he came in?" Clint asked.

Steve shook his head. "I don't think so."

"So what do we do now?" Bruce asked slowly. "How do we find out the truth without letting him know that we know something?"

Steve sighed. "I don't know."

Natasha raised an eyebrow. "You could try when you go with him now."

"How?" Clint said.

"Talk to him. Act casual, like nothing is wrong. Then bring something up about Shield. Make it up. See if he grabs onto the information. If he's a spy for Hydra, then he'll be looking for any information he can get," Natasha said.

"And if he doesn't?" Steve asked.

"Then we'll think of something else to make him squeal", Clint said darkly.

"Don't be morbid, Clint. Tony is still our friend," Steve said sternly. "He's just...made a mistake."

Clint laughed without humour. "This is more than a mistake, Steve. It's plain betrayal. We never knew the real Tony. This is just some facade he made up. He's just a monster wearing a mask of a friend that never existed."

"Clint!" Natasha said reproachfully, but Clint had got up and was walking away from them.

Tony reappeared in the doorway just as Clint passed him, not looking at the genius and disappearing into the hallway. Tony looked at the others, his expression puzzled.

"Ready to go?" He asked slowly, looking at Steve with unsure eyes.

_'He's just a monster wearing a mask of a friend that never existed.'_

Steve nodded, standing up. "Yeah, lets go."


	4. Chapter 4

"Holy fuck! Thank gods I bought a coat, huh?"

Tony laughed after he had spoken, his breath fogging up from the cold. Steve glanced at Tony, how pink the geniuses face had gotten from the cold air. He had put his coat on just before they had stepped outside which was cold as heck in the winter.

Snow fell around them, freezing the air around them, making the lungs burn as they breathed in the cold air. Their feet crunching on the snow as they walked down the sidewalk side by side together.

"Language," Steve said out of habit before shutting up, knowing that Tony would make fun.

Tony looked like he was trying not to laugh at him. "Are you ever going to stop saying that?"

"Probably not," Steve admitted with a wry smile at his genius friend.

Tony grinned and they walked in silence for a few minutes, not as if it were uncomfortable, but just a calm, comfortable silence.

Finally they arrived at the coffee shop, Tony saying he just wanted a coffee and he'd find them a spot to sit as Steve went to place their order.

After making the order with the girl behind the counter, he went over to where Tony sat near a large window, the snow falling outside.

"This isn't too bad," Tony mumbled, almost to himself. "If I had known it were this easy to go outside I would have done it ages ago!"

"So, you'll do it more often now?" Steve inquired, a smile tugging at his lips.

Tony snorted. "Hell no. Physical exercise isn't really my thing. Well, depending on the exercise in question," Tony said with a not-so-subtle wink.

Steve rolled his eyes at Tony's charm. If Tony wasn't an Alpha, Steve would have thought Tony was flirting with him. He wished he was. Steve shook his head, trying to get rid of his thoughts. "One day, you'll make an Omega really happy, Tones."

Tony raised an eyebrow at that. "You think so?"

Steve nodded. "Yeah. You have the charm. You got the looks. You're caring and open. You're honest..." Steve trailed off, thinking about why he was here. What the others were hoping from him. He couldn't say Tony was honest because it seemed he didn't know the real Tony at all.

"Ah, you're a flirt, Steve,"Tony said with a grin. "What about you? You got your eyes on an Omega?"

The waiter came over, setting down a coffee in front of Tony which the genius instantly took up, drinking from it quickly, probably burning his tongue as he did. Steve got a banana smoothie. He'd never tried one before but he decided to give it a shot. He thanked the waiter who left, leaving them alone again.

Steve shook his head. "Not really," he said thinking of what Natasha had said. Bring up something about Shield. "Too busy sorting through Shield files."

Tony glanced at him over his coffee. "Yeah? How's that going."

Steve bit his lip. "Yeah, good. It's top secret stuff. Fury is trusting me with it. But I know you wouldn't betray me if I told you," he said, taking a sip of his smoothie. He hummed. Not bad. Almost good enough to distract him from the uncomfortable churning in his stomach.

Tony raised an eyebrow at him. "Since when did Captain America break the rules?"

 _'Since when did Ironman spy for Hydra?'_ Steve thought but he just shrugged. "I'm only saying. You're my friend. I know you. You wouldn't lie to me or the others about anything," Steve said, giving Tony a smile which the genius for once, didn't return.

"Of course I wouldn't lie to you," Tony said, quickly looking away, chewing at his lip.

Steve felt his stomach drop. Did Tony not realise how guilty his expression was right now? Or was it part of the act? But why would that be part of the act? Was he meant to suspect him?

"Anyway, like I said, so long as you can keep it a secret, I can tell you," Steve said, trying to keep his voice even.

Tony looked at him and Steve held his breath. He had no idea what Tony would say. What if he said yes? Steve would have to make something up. He also would have to act like nothing was wrong. But how the hell was he meant to do that? His friend might not be his friend at all-

"No, I'm good," Tony said, making Steve's train of thought come to a stop.

"...no?" Steve repeated.

Tony shook his head. "I'm not really interested in all those secret missions and crap. I mean, sure it's cool to maybe have leverage against Fury the asshole he is sometimes, walking me up at four in the morning for missions", Tony grinned at Steve knowing that Steve knew what mission he was talking about. "But I'm not really interested in that stuff. Machines are better. More fun."

Steve slowly nodded. He didn't know what to say to that.

"We should get back", Tony said after a bit of silence. Steve nodded. He couldn't think of anything else to make Tony slip up. That's if there was anything to slip up. Maybe he was right and Tony wasn't working for Hydra. But then why would Tony seem so guilty about Steve saying he wouldn't lie to him?

Tony was hiding something. That much Steve knew. He just didn't know what yet. He needed to talk to the others, get their opinion on this.

Tony stood, offering a hand that wasn't clutching his coffee and Steve gave a slightly forced smile, taking it and allowing himself to be helped up.

He and Tony walked out the coffee shop and back to the Avengers Tower talking about pretty much anything. But Steve's mind was only half on the conversation. The other half was far too preoccupied with dark thoughts and fears. But only one question kept circling Steve's mind.

What was Tony hiding?

**Notes for the Chapter:**

> ⚠️Warning: strong language⚠️


	5. Chapter 5

Tony had thanked Steve for going out with him with a quick "We should do this again some time" before he was rushing off to his lab, leaving Steve standing there looking very confused.

He swallowed, thinking over everything that had happened as he headed to the kitchen, thinking of making some lunch for everyone to distract his thoughts.

What he didn't expect was for all his teammates to be there waiting for him.

Steve looked at them all, chewing his lip as he knew why they were there.

"What happened?" Natasha asked after an awkward silence.

Steve sighed, walking into the kitchen and looking around for bread. "Anyone want a chicken sandwich?" He asked, not answering the question.

Thor hesitantly raised his hand but when no one else did he slowly lowered it again with a disappointed look.

"Stop stalling for time, Steve. What happened?" Clint said a little sharply.

Steve sighed, placing the loaf of bread he'd found on the bench. "Nothing all that important really. We just chatted mostly about random stuff."

"Did you bring up something about Shield?" Natasha asked with a raised eyebrow.

Steve nodded. "Yeah."

"What did you say about it?" Bruce asked curiously. He had hoped he'd been wrong about his science buddy but he wasn't sure what to believe. He had seen what he saw and he couldn't change that no matter how much he wanted to.

"I said it was top secret. I said I could tell him about it because I could trust him knowing about it. That he wouldn't tell anyone," Steve explained, taking out a butter knife from the drawer before going back to the fridge to get some butter and chicken bits.

"And how did he react to that?" Natasha asked, her eyes calculating as she waited for Steve's answer.

Steve looked for longer than was necessary in the fridge for the butter which sat on the shelf right in front of his eyes. Eventually he sighed, taking out the butter as he set in on the table.

"He seemed...nervous, I guess," Steve reluctantly admitted. "He said he'd never lie to me."

Clint snorted. "That's a lie in itself."

Steve glared at him. "It wasn't. He didn't lie...he just pretended being someone he wasn't..." Steve pressed his lips together, a bitter taste in his mouth.

Clint rolled his eyes. "Because that's so much better, isn't it?"

"Be quiet," Natasha scolded the archer. She looked back at Steve, her gaze gentle. "Did he take the bait? The information on Shield? Did he seem interested in it at all?"

Steve thought for a moment. "...not really. I asked him if he wanted to know about it but he said no. Said he wasn't interested. Said he was more interested in machines and stuff."

"Well, he is a mechanic," Bruce pointed out. "So that would make sense."

"Do you think he suspected you knew something?" Natasha asked. "Because, no offense, you're not a great actor."

Steve frowned at her. "I don't think so. He just acted like normal everyday Tony."

"Yeah, well, 'normal everyday Tony' apparently works for Hydra and has likely already betrayed half of the things he knows about Shield to Hydra," Clint said with a scowl.

"We don't know if he even works for Hydra," Steve protested.

"He has their mark literally tattooed to his back! What more proof do you want?" Clint snapped back angrily.

Steve glared, his blue eyes cold. "There could be plenty of reasons why he has it. We don't know everything about Tony."

"Clearly," Clint muttered.

"He just doesn't seem like he'd work for Hydra and he definitely hasn't given any indication that he's spying on us or Shield," Steve said, shaking his head.

"He hacked Shield once, remember?" Bruce said, referring to the time when they were on the helicarrier.

"Yeah, but that was because he thought Shield was up to no good and it turns out he was right. Shield was trying to make a weapon with the tesseract," Steve said, buttering the bread.

"Even so, he still hacked Shield. Who knows what he could have learned from just that alone," Clint said with a grim look.

"I have to say, Clint has a point. We don't know what to expect from Tony. Especially not now considering that we know he has somehow been involved with Hydra," Natasha said, giving Steve a slightly apologetic look.

Steve put the chicken bits onto the buttered bread, internally conflicted. He knew deep down that Natasha was right. One way or another, whether by purpose or by accident, Tony had crossed paths with Hydra. Steve didn't know how to feel about that.

"We just need to be careful what we say around him from now on. We can't let loose any information on Shield or anything else Tony doesn't know about. Not until we get to the bottom of this all. Understood?" Natasha said, looking around at the others who all murmured their confirmation.

"Now that that's sorted," Steve said, finishing the last off the last of the sandwiches, "who wants a sandwich?"

This time, all hands flew up.


End file.
